###### tags: `BIOHACKING`
[TOC]
# Megathread for COVID-19 discussion
Last Updated: 2020-03-17
| [Megathread on HackMD] | [Megathread on Facebook] |
|:-----------------------|:-------------------------|
## Meta
:::danger
**2020-03-17 NOTE:** Launch of something new is imminent. Stay tuned.
**2020-03-14 NOTE:** https://biohacking.metamerlabs.io/
**2020-03-13 NOTE:** This file has reached the limits of HackMD.
It will be migrated to a custom documentation site shortly.
:::
### Staging
<details><summary>Everything messy is hiding here</summary>
#### 2020-03-11 Resources - Handbook Links
These are listed under "Communities and Libraries". Doesn't make sense to me.
- [Andreessen Horowitz library of coronavirus resources](https://a16z.com/2020/03/08/novel-coronavirus-and-covid-19-disease-resources-readings)
- [Chartered Society of Physiotherapists](https://www.csp.org.uk/news/coronavirus-resources-csp-members)
- [Engaging Local Government Leaders Coronavirus Resources](https://elgl.org/covid-19)
- https://www.kaggle.com/search?q=coronavirus
- https://www.producthunt.com/search?q=coronavirus
#### Megathread 2020-03-04 Links
- [CSSEGISandData/COVID-19: Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE](https://github.com/CSSEGISandData/COVID-19)
- [Coronavirus: WHO warns over hoarding medical supplies - BBC News](https://www.bbc.com/news/live/world-51716375)
- [Wei_Dai - LessWrong 2.0](https://www.lesswrong.com/users/wei_dai)
* [Fractal kinetics of COVID-19 pandemic](https://www.medrxiv.org/content/10.1101/2020.02.16.20023820v2.full.pdf)
- [New Covid findings from the report of the WHO expert commission after 9 days in China : europe](https://www.reddit.com/r/europe/comments/fbsray/new_covid_findings_from_the_report_of_the_who/)
#### Megathread 2020-03-03 Links
* [covid.410go.net](http://covid.410go.net/)
* [InfoMullet: Adjusting our Mental-Model of COVID-19](http://infomullet.com/2020/03/02/covid19mentalmodel/)
* [CSSEGISandData/COVID-19: Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE](https://github.com/CSSEGISandData/COVID-19)
* [COVID-19/parameter_estimates/2019_novel_coronavirus at master · midas-network/COVID-19](https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus)
* [Pandemic Xenophobia – qwerky science](https://mad.science.blog/2020/01/29/pandemic-xenophobia/)
* [Johns Hopkins Covid-19 Github Data Repo | Hacker News](https://news.ycombinator.com/item?id=22476834)
* [Coronavirus: Links, Speculation, Open Thread | Slate Star Codex](https://slatestarcodex.com/2020/03/02/coronavirus-links-speculation-open-thread/)
#### CIDRAP List for Merging - COVID-19 Maps & visuals
<ul><li><a href="https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6" target="_blank">Coronavirus COVID-19 global cases</a><span style="font-weight: 400;"> (Johns Hopkins)</span></li><li><a href="https://www.healthmap.org/ncov2019/" target="_blank">Novel coronavirus (COVID-19) outbreak timeline map</a><span style="font-weight: 400;"> (HealthMap)</span></li><li><a href="https://hgis.uw.edu/virus/" target="_blank"><span style="font-weight: 400;">Novel coronavirus infection map</span></a><span style="font-weight: 400;"> (University of Washington)</span></li><li><span style="font-weight: 400;"><a href="http://nssac.bii.virginia.edu/covid-19/dashboard/" target="_blank">COVID-19 surveillance dashboard</a> (University of Virginia)</span></li><li><span style="font-weight: 400;"><a href="http://who.maps.arcgis.com/apps/opsdashboard/index.html#/c88e37cfc43b4ed3baf977d77e4a0667" target="_blank">Novel coronavirus (COVID-19) situation dashboard</a> (WHO)</span></li><li><span style="font-weight: 400;"><a href="https://www.cdc.gov/coronavirus/2019-ncov/cases-in-us.html" target="_blank">Coronavirus disease 2019 (COVID-19) in the US</a> (CDC)</span></li><li><span style="font-weight: 400;"><a href="https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases" target="_blank">Geographical distribution of COVID-19 cases worldwide</a> (ECDC)</span></li><li><span style="font-weight: 400;"><a href="https://www.kff.org/global-health-policy/fact-sheet/coronavirus-tracker/" target="_blank">COVID-19 coronavirus tracker</a> (Kaiser Family Foundation)</span></li><li><span style="font-weight: 400;"><a href="https://www.worldometers.info/coronavirus/" target="_blank">COVID-19 coronavirus oubreak</a> (Worldometer)</span></li><li><span style="font-weight: 400;"><a href="https://multimedia.scmp.com/infographics/news/china/article/3047038/wuhan-virus/index.html?src=article-launcher" target="_blank">Coronavirus: the new disease Covid-19 explained</a> (</span><em><span style="font-weight: 400;">South China Morning Post</span></em><span style="font-weight: 400;">)</span></li><li><a href="https://storymaps.arcgis.com/stories/4fdc0d03d3a34aa485de1fb0d2650ee0" target="_blank" class="clutterFree_existingDuplicate clutterFree_noIcon cf_div_theme_dark"><span style="font-weight: 400;">Mapping the Wuhan coronavirus outbreak</span></a><span style="font-weight: 400;"> (Esri StoryMaps)</span></li></ul>
### TODOs
- [ ] Add Megathread 2020-03-03 Links
- [ ] add wuxia diagnostics
- [ ] add decibio blogpost
- [ ] Public Health England (PHE): does it have protocols, or just biosafety stuff?
- https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories
- [ ] Add case indices
- [ ] [BHO News table](https://bnonews.com/index.php/2020/02/the-latest-coronavirus-cases/)
- [ ] Add CIDRAP
- [ ] [CIDRAP Bibligraphy](http://www.cidrap.umn.edu/infectious-disease-topics/covid-19)
- [ ] [CIDRAP Tools](http://www.cidrap.umn.edu/covid-19/tools)
- [ ] [CIDRAP Lab & Diagnostics](http://www.cidrap.umn.edu/covid-19/lab-guidance-diagnostics)
- [ ] [CIDRAP Maps & Visuals](http://www.cidrap.umn.edu/covid-19/maps-visuals)
- rounds up all the stuff like worldometer, Johns Hopkins, etc.
### Facebook Edition (for pasting)
==Jeremy Note: this is for editing the post on facebook. Fb can do a limited amount of text formatting now, but (a) only in groups + Workplace and (b) any tweak to previously-formatted text causes garbled bullshit to render on mobile. This usually happens when someone pastes a link while drafting a post on desktop and unwittingly lets facebook interpret it as markdown, not realizing that mobile users see garbage. The trick is wholesale replacement of the previous content with new content every time.==
<details>
**Megathread for COVID-19 discussion**
Here is a containment thread for all things COVID-19.
**[Megathread on Hackmd]** - where all the stuff is!
\# [Resources and References]
[Experts]
[Virological]
[Zotero group (library) and feed]
\# [News and Updates]
[Event Cancellations and Postponements]
[OpenCell Post]
[Other threads in this group]
\# **[Protocols]**
[Summary table of available protocols]
[charite.de]
[chinacdc.cn]
[cdc.gov - Testing Issues - Mainstream Reporting]
[cdc.gov - Testing Protocols and Primers]
[hku.hk]
[niid.go.jp]
[nih.moph.go.th]
[other .gov (US)]
\# [WHO Protocols List - Notes by country/institute]
[CDC Bungled Test Kit]
\# [Vaccines] (WIP)
**AKA**
- 2019-nCoV
- COVID-2019, COVID-19, COVID19
- (the disease)
- Corona virus, Coronavirus
- SARS-CoV-2 (the virus)
- Wuhan Flu, Wuhan Virus
**Thread Rationale**
1. Pandemic news is of general importance, but of tangential relevance to biohacking in most cases.
2. SARS was major world news for 18 months. MERS has had three notable outbreaks from 2012 to 2018. There's no particular reason to expect news to abate anytime soon.
3. Aiming to keep coronavirus discussion to one thread limits spam without forcing an outright ban on the topic.
</details>
</details>
## About
Here is a containment thread for all things COVID-19.
### AKA
(The [use-mention distinction](https://en.wikipedia.org/wiki/Use%E2%80%93mention_distinction) applies, ofc.)
- Formal Jargon
- the virus
- 2019-nCoV
- SARS-CoV-2
- the disease
- COVID-19
- COVID-2019
- COVID19
- Colloquial Terms
- twitter.com
- [CoronaAlert](https://twitter.com/hashtag/CoronaAlert)
- [CoronaOutbreak](https://twitter.com/hashtag/CoronaOutbreak)
- [Coronavirus](https://twitter.com/hashtag/Coronavirus)
- [Coronvirus](https://twitter.com/hashtag/Coronvirus)
- three distinct uses as of 2020-03-04:
- as a misspelling
- as a censorship-circumvention hashtag
- as a parody hashtag, e.g. posts about DIY gimp masks
- [COVID](http://twitter.com/hashtag/covid)
- [COVID19](https://twitter.com/hashtag/covid19)
- [COVID-19](https://twitter.com/hashtag/covid-19)
- [COVID_19](https://twitter.com/hashtag/COVID_19)
- 4chan.org
- coronachan
- General
- Corona virus
- Coronavirus
- Kung Flu
- Wuhan Flu
- Wuhan Virus
### Thread Rationale
1. Pandemic news is of general importance, but of tangential relevance to biohacking in most cases.
2. SARS was major world news for 18 months. MERS has had three notable outbreaks from 2012 to 2018. There's no particular reason to expect news to abate anytime soon.
3. Aiming to keep coronavirus discussion to one thread limits spam without forcing an outright ban on the topic.
## Resources
### Communities
- [CoronavirusNetwork.org](http://www.coronavirusnetwork.org/)
- [Discord - Biohacker Coronavirus Task Force](https://discord.gg/9Nevs2)
- [EndCoronavirus.org](https://www.endcoronavirus.org/)
- [Facebook - Viral Exploration](https://www.facebook.com/groups/183132532752588/)
- [Google Group - DIYBio](https://groups.google.com/forum/#!topic/diybio/F_y2WsfEJog)
- [JOGL open-source detection protocol](https://app.jogl.io/project/118#about)
- [Reddit - r/coronavirus](https://www.reddit.com/r/coronavirus)
- [Reddit - r/COVID19](https://www.reddit.com/r/COVID19)
- [Slack - London biohackspace - \#lets-beat-corona](http://biohackspace.org/slack)
- [Twitter - \#coronavirus resources](https://twitter.com/search?q=%22coronavirus%20resources%22)
- [Whatsapp - CoronavirusTechChat](https://bit.ly/CoronavirusTechChat)
- [Whatsapp - CoronavirusTechRandomChat](https://bit.ly/CoronavirusTechRandomChat)
<div class="list-container">
<div class="list-title"><h3>Experts on twitter</h3></div>
<div class="list-section">twitter.com</div>
<ul>
<li><mark>Jeremy Note: a few of these people came recommended via a twitter thread about identifying experts on the topic to follow. Feel free to recommend more.</mark></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/MackayIM" target="_blank">ɪᴀɴ ᴍ ᴍᴀᴄᴋᴀʏ, ᴘʜᴅ 🦠🤧🧬🥼🦟 (@MackayIM) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/KindrachukJason" target="_blank">Jason Kindrachuk (@KindrachukJason) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/angie_rasmussen" target="_blank">Dr. Angela Rasmussen (@angie_rasmussen) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/GeopoliticalJD" target="_blank">GeopoliticalJD (@GeopoliticalJD) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://mobile.twitter.com/alexandraphelan" target="_blank">Dr Alexandra Phelan (@alexandraphelan) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/HelenBranswell" target="_blank">Helen Branswell (@HelenBranswell) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/DrMay5" target="_blank">Meghan May (@DrMay5) / Twitter</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/IsabelOtt" target="_blank">Isabel Ott (@IsabelOtt) / Twitter</a></li>
</ul>
</div>
<div class="list-container">
<div class="list-title"><h3>Reference Sites</h3></div>
<div class="list-section"><h4>virological.org</h4></div>
<ul>
<li><mark>Jeremy Note: virological.org has a category dedicated to this topic, and three subcategories.<br>This is a high-quality site.</mark></li>
<li><img class="sb-favicon" src="http://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"><a href="http://virological.org/" target="_blank">Home - Virological</a></li>
<li><img class="sb-favicon" src="http://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"><a href="http://virological.org/c/novel-2019-coronavirus/33" target="_blank">Latest Novel 2019 coronavirus topics - Virological</a></li>
<ul>
<li><img class="sb-favicon" src="http://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"><a href="http://virological.org/c/novel-2019-coronavirus/ncov-2019-evolutionary-history/35" target="_blank">Latest Novel 2019 coronavirus/nCoV-2019 Evolutionary History topics - Virological</a></li>
<li><img class="sb-favicon" src="http://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"><a href="http://virological.org/c/novel-2019-coronavirus/ncov-2019-genomic-epidemiology/36" target="_blank">Latest Novel 2019 coronavirus/nCoV-2019 Genomic Epidemiology topics - Virological</a></li>
<li><img class="sb-favicon" src="http://virological.org/uploads/default/optimized/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623_2_32x32.png"><a href="http://virological.org/c/novel-2019-coronavirus/ncov-2019-diagnostics-and-vaccines/37" target="_blank">Latest Novel 2019 coronavirus/nCoV-2019 Diagnostics and Vaccines topics - Virological</a></li>
</ul>
</ul>
<div class="list-section"><h4>zotero.org</h4></div>
<ul>
<li><mark>Jeremy Note: The zotero group (reference library) now requires membership to view stuff. So I made an API key and created a feed for it. It's embedded in the hackpad for convenience. You can also click the heading above to open a standalone webpage. Or subscribe as RSS, if you're like that.</mark></li>
<li><mark>Zotero group is run by Alexandra Phelan.</mark></li>
<li><img class="sb-favicon" src="https://www.inoreader.com/favicon.ico"><a href="https://www.inoreader.com/stream/user/1006233461/tag/Megathread_for_COVID-19_Zotero/view/html?t=Feed%20of%202019-nCoV%20Zotero%20group%20for%20Megathread&l=https%3A%2F%2Ffiles.catbox.moe%2Fjlm1ij.jpg&n=999&w=710&lw=50&lh=50" target="_blank">Feed of 2019-nCoV Zotero group for Megathread</a></li>
<li><img class="sb-favicon" src="https://www.zotero.org/favicon.ico"><a href="https://www.zotero.org/groups/2436126/ncov2019" target="_blank">Zotero | Groups > nCoV2019</a></li>
</ul>
</div>
<details><summary>Zotero group iframe - click to display.</summary><iframe width="730" height="800" src="https://www.inoreader.com/stream/user/1006233461/tag/Megathread_for_COVID-19_Zotero/view/html?t=Feed%20of%202019-nCoV%20Zotero%20group%20for%20Megathread&l=https%3A%2F%2Ffiles.catbox.moe%2Fjlm1ij.jpg&n=999&w=710&lw=50&lh=50" frameborder="0" tabindex="-1"></iframe></details>
## News and Updates
### Event Cancellations and Postponements
- ==Jeremy Note: Josiah Zayner's stance on cancelling BioHTP==
- ["over my dead body"](https://www.facebook.com/josiah.zayner/posts/10104553811332757?comment_id=10104553876547067)
- ==Jeremy Note: There are far too many events across too many topic areas to track here. Someone has spun out a new site for this purpose as of 2020-03-04. Its initial content appears to have been primarily sourced from Hacker News.==
- [**isitcanceledyet.com**](https://isitcanceledyet.com/)
- Links from 2020-03-04 and earlier
- [Tokyo Olympics “looking at a cancellation” if coronavirus not contained](https://news.ycombinator.com/item?id=22420148)
- [Wikipedia Summit 2020 cancelled](https://meta.wikimedia.org/wiki/Wikimedia_Summit_2020)
- [GDC 2020 postponed and/or cancelled](https://polygon.com/2020/2/28/21156431/gdc-2020-canceled-postponed-coronavirus-epic-games-unity-playstation-ea-activision-blizzard-covid-19)
- [APS March Meeting](https://news.ycombinator.com/item?id=22471730)
- [AsiaBSDCon 2020](https://news.ycombinator.com/item?id=22470896)
- [Google Cloud Next 2020 – in person event cancelled](https://news.ycombinator.com/item?id=22470540)
- [Adobe Summit Cancelled](https://news.ycombinator.com/item?id=22470462)
- [Nvidia's GTC Cancelled](https://news.ycombinator.com/item?id=22467317)
- [American Airlines waives change fees as United braces for flight cancellations](https://news.ycombinator.com/item?id=22460845)
- [Nearly 10k sign petition calling for SXSW to be canceled](https://news.ycombinator.com/item?id=22460042)
- [Amazon Cancels On-Site Job Interviews over Covid-19, Ask Workers to Avoid Travel](https://news.ycombinator.com/item?id=22454857)
- [Shopify cancels Unite 2020 conference due to Covid-19](https://news.ycombinator.com/item?id=22444448)
- [Facebook cancels in-person portion of F8 due to Coronavirus](https://news.ycombinator.com/item?id=22435772)
### OpenCell Post (Now Removed)
<div class="list-container">
<div class="list-title">News and Updates</div>
<div class="list-section">opencell.bio</div>
<ul>
<li><mark>Jeremy Note: Linked by Vittorio originally. Original post on opencell was removed and no public archives had it. I plucked it from the void and excerpted just the resources section (culled the pontificating on spanish flu).</mark></li>
<li><mark>The links below are items linked by the now-dead blogpost. The blogpost is below that.</mark></li>
<li><img class="sb-favicon" src="https://www.google.com/s2/favicons?domain=webcache.googleusercontent.com"><a href="https://archive.is/81miA" target="_blank">Blog</a></li>
<li><img class="sb-favicon" src="https://abs.twimg.com/favicons/twitter.ico"><a href="https://twitter.com/mugecevik/status/1222164778069700618" target="_blank">dr muge cevik on Twitter: "@NEJM @tsrabbit3 Based on 34 confirmed #2019nCoV cases that were detected outside Wuhan, Backer et al. estimate the mean incubation period to be 5.8 (4.6 - 7.9, 95% CI) days, ranging from 1.3 to 11.3 days (2.5th to 97.5th percentile). #IDTwitter https://t.co/aYeHUiwRWy https://t.co/5JlXTT48Iu" / Twitter</a></li>
<li><img class="sb-favicon" src="https://cdn.elsevier.io/verona/includes/favicons/favicon-32x32.png"><a href="https://www.elsevier.com/life-sciences/journals/modelling-epidemics-the-maths-behind-disease-outbreaks" target="_blank">Modelling epidemics: the maths behind disease outbreaks</a></li>
<li><img class="sb-favicon" src="https://github.githubassets.com/favicon.ico"><a href="https://github.com/s-andrews/virusbreak" target="_blank">s-andrews/virusbreak: A web based game to simulate virus outbreaks</a></li>
<li><img class="sb-favicon" src="https://cdn.ndemiccreations.com/image/80-h16.jpeg"><a href="https://www.ndemiccreations.com/en/22-plague-inc" target="_blank">Plague Inc. - Ndemic Creations</a></li>
<li><img class="sb-favicon" src="http://www.gleamviz.org/wp-content/themes/gleamviz-v3/favicon.ico"><a href="http://www.gleamviz.org/simulator/" target="_blank">GLEAMviz.org – Simulator</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://www.shanghaitech.edu.cn/2020/0126/c1001a50145/page.htm" target="_blank">上科大和中科院上海药物所联合团队预先公布新型肺炎冠状病毒3CL水解酶高分辨率晶体结构</a></li>
<li><img class="sb-favicon" src="http://www.rcsb.org/favicon.ico"><a href="http://www.rcsb.org/structure/6LU7" target="_blank">RCSB PDB - 6LU7: The crystal structure of COVID-19 main protease in complex with an inhibitor N3</a></li>
<li><img class="sb-favicon" src="http://www.rcsb.org/pdb/img/pdb.ico"><a href="http://www.rcsb.org/pdb/results/static.do;jsessionid=9E900181C2245329609C62E3CC547865?p=results/session_timeout.html" target="_blank">RCSB PDB</a></li>
<li><img class="sb-favicon" src="https://www.biorxiv.org/sites/default/files/images/favicon.ico"><a href="https://www.biorxiv.org/content/10.1101/2020.01.24.919241v3" target="_blank">From SARS-CoV to Wuhan 2019-nCoV Outbreak: Similarity of Early Epidemic and Prediction of Future Trends | bioRxiv</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://glue-tools.cvr.gla.ac.uk/#/home" target="_blank">glue-tools.cvr.gla.ac.uk/#/home</a></li>
<li><img class="sb-favicon" src="https://github.githubassets.com/favicon.ico"><a href="https://github.com/giffordlabcvr" target="_blank">R. Gifford Lab (CVR)</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://nglviewer.org/#nglview" target="_blank">NGL Viewer Projects</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://www.choderalab.org/research-projects/automated-ligand-design" target="_blank">Automated ligand design — Chodera lab // MSKCC</a></li>
<li><img class="sb-favicon" src="https://www.bakerlab.org/wp-content/uploads/2015/11/cropped-logo-1200x1200-32x32.png"><a href="https://www.bakerlab.org/" target="_blank">Main - The Baker Lab</a></li>
<li><img class="sb-favicon" src="https://www.rosettacommons.org/sites/default/files/logo-16_0.png"><a href="https://www.rosettacommons.org/" target="_blank">Welcome to RosettaCommons | RosettaCommons</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="https://collinslab.mit.edu/files/cell_pardee3.pdf" target="_blank">Portable, On-Demand Biomolecular Manufacturing</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="https://collinslab.mit.edu/files/cell_pardee2.pdf" target="_blank">Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="https://collinslab.mit.edu/publications.html" target="_blank">MIT: Collins Lab</a></li>
<li><img class="sb-favicon" src="https://www.pardeelab.org/favicon.ico"><a href="https://www.pardeelab.org/publications.html" target="_blank">pardeelab.org/publications - PARDEE LAB</a></li>
<li><img class="sb-favicon" src="https://journals.plos.org/plosone/resource/img/favicon.ico"><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196484" target="_blank">Computational identification, characterization and validation of potential antigenic peptide vaccines from hrHPVs E6 proteins using immunoinformatics and computational systems biology approaches</a></li>
<li><img class="sb-favicon" src="http://www.justbiotherapeutics.com/wp-content/uploads/2017/03/cropped-Jdot-32x32.jpg"><a href="http://www.justbiotherapeutics.com/technology" target="_blank">Technology | Just.</a></li>
</ul>
</div>
<mark>Blogpost excerpt begins</mark>
Understanding the situation is important and combatting misinformation even more so. Social media is (actually) useful here. **[This thread][opencell_01]** combines some valuable scientific insights. Below are are some resources that can help to dig a little deeper:
**Resources for understanding the spread:**
- A great, simple and down to earth **review of the math behind epidemic modelling** covered by **[Elsevier][opencell_02]**. Great start.
- **[Virus simulator][opencell_03]:** This is developed by Simon Andrews and his GitHub is packed with useful repos (including Fast QC for high throughput sequencing analysis). Unfortunately the virus simulator doesn’t do a great job of explaining the background calculations.
- [Plague inc][opencell_04] is a bit more of an actual game. But remains terrifyingly realistic..
- [GLEAMviz][opencell_05] has a pretty sweet (and advanced) modelling tool for global epidemics. It is quite a serious tool.
**Understand the genetics:**
- The **DNA sequence is free to download on the [genbank database][opencell_06].**
- The protein crystal structure has already been studied ([press release in Mandarin][opencell_07]) and is apparently available directly from the researcher. The protein data bank ([PDB][opencell_08]) number is 6LU7 but is listed as unavailable. Seems strange they would not share this data..
- A recent paper comparing SARs and 2019 nCoV is available on [BioRxiv][opencell_09].
- Singer et al, (from the Gifford Lab) have developed [GLUE][opencell_10] a tool for studying the evolution of viruses and that is worth exploring. Their [GitHub page][opencell_11] is a bit all over the place but definitely worth exploring if you are knowledgable in the area.
- [NGL Viewer][opencell_11]: a web application for molecular visualization
- Cant say this is totally applicable but the Chodera Lab is incredible. They have some work on [ligand design][opencell_12] and mostly focus on computational design of small molecules.
**Developing vaccines/detection or other intervention:**
- The **[Baker lab][opencell_13]** in U Washington is a world leader here. They developed the well-known and popular **[Rosetta][opencell_14] protein modelling software.**
- **Huge potential for [on demand vaccines][opencell_15], [virus detection][opencell_16] and riboswitches are coming out of the [Collin’s Lab][opencell_17] (MIT) and the lead author (Keith Pardee) on those now has a [group at UoT][opencell_18].**
- Computation design of vaccines is a HOT topic and should be a great application of our societies computing power. Work from [Khan et al.][opencell_19] looks impressive.
- Lots of companies are “CHANGING THE WORLD” (quotes imply great cynicism and eye rolling) and a few (e.g., [exotec biologics][opencell_20]) are applying (you guessed it!) machine learning to vaccine development. It is unclear if this is for real.
### Other threads in Biohacking and Genetic Design Network
| Date | Post Link |
|------------|--------------------|
| 2020-03-12 | [1588958661242813] |
| 2020-03-12 | [1588875774584435] |
| 2020-03-12 | [1588518901286789] |
| 2020-03-11 | [1587933708011975] |
| 2020-03-10 | [1586670104805002] |
| 2020-03-08 | [1585257061612973] |
| 2020-03-06 | [1583364041802275] |
| 2020-03-04 | [1582033708601975] |
| 2020-03-04 | [1581425731996106] |
| 2020-03-01 | [1578910642247615] |
| 2020-02-29 | [1577981212340558] |
| 2020-02-29 | [1577925299012816] |
| 2020-02-27 | [1576195075852505] |
| 2020-02-24 | [1573924052746274] |
| 2020-02-05 | [1556781941127152] |
| 2020-01-31 | [1552794401525906] |
| 2020-01-31 | [1552129371592409] |
| 2020-01-30 | [1551677334970946] |
| 2020-01-30 | [1551512468320766] |
| 2020-01-30 | [1551295665009113] |
| 2020-01-30 | [1551207721684574] |
| 2020-01-29 | [1550526101752736] |
| 2020-01-29 | [1550506698421343] |
| 2020-01-28 | [1550257578446255] |
| 2020-01-28 | [1550016768470336] |
| 2020-01-28 | [1549966398475373] |
| 2020-01-28 | [1549815391823807] |
| 2020-01-28 | [1549721555166524] |
| 2020-01-27 | [1548838048588208] |
| 2020-01-27 | [1548802785258401] |
| 2020-01-26 | [1548442805294399] |
| 2020-01-26 | [1548408148631198] |
| 2020-01-26 | [1548052875333392] |
| 2020-01-26 | [1547918345346845] |
| 2020-01-25 | [1547217105416969] |
| 2020-01-25 | [1547156925422987] |
| 2020-01-25 | [1547142058757807] |
| 2020-01-24 | [1546598995478780] |
| 2020-01-24 | [1546596108812402] |
| 2020-01-24 | [1546500112155335] |
| 2020-01-23 | [1545456302259716] |
| 2020-01-23 | [1545436955594984] |
| 2020-01-23 | [1545104242294922] |
| 2020-01-23 | [1545090018963011] |
| 2020-01-22 | [1544189262386420] |
| 2020-01-21 | [1543505329121480] |
| 2020-01-20 | [1542801252525221] |
## Protocols
### Molecular assays to diagnose 2019-nCoV
Several assays that detect the 2019-nCoV have been and are currently under development, both *in-house* and commercially. Some assays may detect only the novel virus and some may also detect other strains (e.g. SARS-CoV) that are genetically similar.
### In-house developed molecular assays
Some groups shared their protocols which can be accessed below (Summary table and link to the protocols). In some cases, the groups will be willing to send reagents or reagent mixes prepared in their laboratories, with or without associated fees. It is strongly recommended to contact the developer if you need further assistance. The list is not exhaustive and is being updated regularly.
#### Summary table of available protocols
<table style=""><tbody><tr style="height:16.6667%;"><td style="width:33.3333%;text-align:left;"><strong>Country</strong></td><td style="width:33.3333%;text-align:left;"><strong>Institute</strong></td><td style="width:33.3333%;text-align:left;"><strong>Gene targets</strong></td></tr><tr style="height:16.6667%;"><td style="width:33.333333333333336%;">China</td><td style="width:33.333333333333336%;">China CDC</td><td style="width:33.333333333333336%;">ORF1ab and N</td></tr><tr style="height:16.6667%;"><td style="width:33.3333%;">Germany</td><td style="width:33.333333333333336%;">Charité</td><td style="width:33.333333333333336%;">RdRP, E, N</td></tr><tr style="height:16.6667%;"><td style="width:33.333333333333336%;">Hong Kong</td><td style="width:33.333333333333336%;">HKU</td><td style="width:33.333333333333336%;">ORF1b-nsp14, N</td></tr><tr style="height:16.6667%;"><td style="width:33.3333%;">Japan</td><td style="width:33.333333333333336%;">National Institute of Infectious Diseases, Department of Virology III</td><td style="width:33.333333333333336%;">Pancorona and multiple targets, Spike protein</td></tr><tr style="height:16.6667%;"><td style="width:33.3333%;">Thailand</td><td style="width:33.333333333333336%;">National Institute of Health</td><td style="width:33.333333333333336%;">N</td></tr><tr style="height:16.666666666666668%;"><td style="width:33.333333333333336%;">US</td><td style="width:33.3333%;">US CDC</td><td style="width:33.333333333333336%;">Three targets in N gene</td></tr></tbody></table>
<div class="list-container">
<div class="list-title"><h3>WHO Protocols List</h3></div>
<div class="list-section"><h4>charite.de</h4></div>
<ul>
<li><img class="sb-favicon" src="https://virologie-ccm.charite.de/typo3conf/ext/charite_site/Resources/Public/Icon/favicon.ico"><a href="https://virologie-ccm.charite.de/en/diagnostics/consultant_laboratory_for_coronaviruses/" target="_blank">Consultant Laboratory for Coronaviruses: Institute of Virology - Charité – Universitätsmedizin Berlin</a></li>
<li><img class="sb-favicon" src="https://www.european-virus-archive.com/sites/default/files/favicon_0.ico"><a href="https://www.european-virus-archive.com/" target="_blank">EVAg | European Virus Archive - GLOBAL</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="https://www.gisaid.org/" target="_blank">GISAID - Global Initiative on Sharing All Influenza Data</a></li>
<li><img class="sb-favicon" src="http://www.google.com/s2/favicons?domain_url=https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf?sfvrsn=a9ef618c_2"><a href="https://www.who.int/docs/default-source/coronaviruse/protocol-v2-1.pdf?sfvrsn=a9ef618c_2" target="_blank">Diagnostic detection of 2019-nCoV by real-time RT-PCR | Charité</a></li>
</ul>
<div class="list-section"><h4>chinacdc.cn</h4></div>
<ul>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html" target="_blank">新型冠状病毒核酸检测引物和探针序列（Specific primers and probes for detection 2019 novel coronavirus）</a></li>
</ul>
<div class="list-section"><h4>cdc.gov - Testing Issues - Mainstream Reporting</h4></div>
<ul>
<li><img class="sb-favicon" src="https://www.nationalreview.com/wp-content/themes/national-review/static/images/favicons/favicon-32x32.png"><a href="https://www.nationalreview.com/news/cdc-refused-to-test-first-possible-community-transmitted-coronavirus-case-for-days/" target="_blank">California Coronavirus -- CDC Refused to Test First Possible Community-Transmitted Case for Days | National Review</a></li>
<li><img class="sb-favicon" src="https://www.nytimes.com/vi-assets/static-assets/favicon-4bf96cb6a1093748bf5b3c429accb9b4.ico"><a href="https://www.nytimes.com/2020/02/27/health/coronavirus-testing-california.html" target="_blank">Coronavirus Diagnosis in California Highlights Testing Flaws - The New York Times</a></li>
<li><img class="sb-favicon" src="https://assets.propublica.org/prod/v3/images/favicon.ico"><a href="https://www.propublica.org/article/cdc-coronavirus-covid-19-test" target="_blank">Key Missteps at the CDC Have Set Back Its Ability to Detect the Potential Spread of Coronavirus — ProPublica</a></li>
<li><img class="sb-favicon" src="https://assets.guim.co.uk/images/favicons/46bd2faa1ab438684a6d4528a655a8bd/32x32.ico"><a href="https://www.theguardian.com/world/2020/feb/25/coronavirus-outbreak-severe-disruption-america-cdc-united-states" target="_blank">Coronavirus could cause 'severe disruption' in America, CDC says | World news | The Guardian</a></li>
</ul>
<div class="list-section"><h4>cdc.gov - Testing Protocols and Primers</h4></div>
<ul>
<li><img class="sb-favicon" src="http://www.google.com/s2/favicons?domain_url=https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-for-detection-instructions.pdf"><a href="https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-for-detection-instructions.pdf" target="_blank">Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus - Instructions for Use - PDF | CDC</a></li>
<li><img class="sb-favicon" src="http://www.google.com/s2/favicons?domain_url=https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf"><a href="https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf" target="_blank">2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes - PDF | CDC</a></li>
<li><img class="sb-favicon" src="https://www.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html" target="_blank">Real-Time RT-PCR Panel for Detection 2019-nCoV | CDC</a></li>
<li><img class="sb-favicon" src="https://www.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html" target="_blank">2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes - HTML | CDC</a></li>
</ul>
<div class="list-section"><h4>fightcovid.hku.hk; med.hku.hk</h4></div>
<ul>
<li><img class="sb-favicon" src="https://fightcovid19.hku.hk/content/uploads/2020/02/cropped-fav-1-32x32.jpg"><a href="https://fightcovid19.hku.hk/#" target="_blank">HKU takes on COVID-19, the novel coronavirus - HKU Takes on covid-19, the Novel Coronavirus</a></li>
<li><img class="sb-favicon" src="https://fightcovid19.hku.hk/content/uploads/2020/02/cropped-fav-1-32x32.jpg"><a href="https://fightcovid19.hku.hk/detection-of-2019-novel-coronavirus-2019-ncov-in-suspected-human-cases-by-rt-pcr/" target="_blank">[World Health Organization] Detection of COVID-19 in suspected human cases by RT-PCR - HKU Takes on covid-19, the Novel Coronavirus</a></li>
<li><img class="sb-favicon" src="https://fightcovid19.hku.hk/content/uploads/2020/02/cropped-fav-1-32x32.jpg"><a href="https://fightcovid19.hku.hk/research/" target="_blank">Research - HKU Takes on covid-19, the Novel Coronavirus</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="https://www.med.hku.hk/en/The-Latest-from-HKUMed-on-COVID-19" target="_blank">HKU Li Ka Shing Faculty of Medicine</a></li>
<li><img class="sb-favicon" src="https://www.who.int/favicon.ico"><a href="https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4" target="_blank">Microsoft Word - 2019-nCoV protocol HKU clean for posting.doc</a></li>
</ul>
<div class="list-section"><h4>niid.go.jp</h4></div>
<ul>
<li><img class="sb-favicon" src="https://www.niid.go.jp/niid/templates/gk_memovie/images/favicon.ico"><a href="https://www.niid.go.jp/niid/en/2013-03-15-04-55-59/2483-disease-based/ka/corona-virus/2019-ncov/9334-ncov-vir3-2.html" target="_blank">Detection of second case of 2019-nCoV infection in Japan</a></li>
<li><img class="sb-favicon" src="https://www.who.int/favicon.ico"><a href="https://www.who.int/docs/default-source/coronaviruse/method-niid-20200123-2.pdf?sfvrsn=fbf75320_7" target="_blank">Method_NIID_20200123_w_Erratum</a></li>
</ul>
<div class="list-section"><h4>nih.moph.go.th</h4></div>
<ul>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://nih.dmsc.moph.go.th/indexeng.html" target="_blank">National Institute of Health of Thailand</a></li>
<li><img class="sb-favicon" src="https://sessionbuddy.com/images/default.png"><a href="http://www.moph.go.th/" target="_blank">www.moph.go.th</a></li>
<li><img class="sb-favicon" src="https://en.wikipedia.org/static/favicon/wikipedia.ico"><a href="https://en.wikipedia.org/wiki/Ministry_of_Public_Health_(Thailand)" target="_blank">Ministry of Public Health (Thailand) - Wikipedia</a></li>
<li><img class="sb-favicon" src="https://www.who.int/favicon.ico"><a href="https://www.who.int/docs/default-source/coronaviruse/conventional-rt-pcr-followed-by-sequencing-for-detection-of-ncov-rirl-nat-inst-health-t.pdf?sfvrsn=42271c6d_4" target="_blank">เอกสารประกอบการตรวจหาสารพันธุกรรมไวรัส MERs-CoV ด้วยวิธี Real time RT-PCR</a></li>
</ul>
<div class="list-section"><h4>other .gov (US)</h4></div>
<ul>
<li><img class="sb-favicon" src="https://www.medicalcountermeasures.gov/assets/img/favicon.ico"><a href="https://www.medicalcountermeasures.gov/" target="_blank">MedicalCountermeasures.gov</a></li>
<li><img class="sb-favicon" src="https://www.internationalreagentresource.org/Portals/6/irr_icon.ico?ver=2017-06-01-151850-817"><a href="https://www.internationalreagentresource.org/Catalog.aspx?q=2019-nCoV&f_displaysearchname=Kits&page=1&f_organism=Non-influenza%2bpanel" target="_blank">IRR: Advanced Catalog Search</a></li>
</ul>
</div>
### WHO Protocols List - Notes by country/institute
- China (China CDC)
- Germany (Charité)
- Hong Kong (HKU)
- [HKU (Peiris et al.) - Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR]
- Japan (National Institute of Infectious Diseases, Department of Virology III)
- Nao et al.
- Thailand (National Institute of Health)
- bizarre document
- US (US CDC)
- see section below
#### CDC Bungled Test Kit
<div class="list-container">
<div class="list-title">CDC Errata</div>
<div class="list-section"><h4>Document Title Errors</h4></div>
<ul>
<li><mark>Jeremy Note: The titles of CDC's PDFs are often wrong, since they borrow from other files while compiling them. Examples:</mark></li>
<li>URL: https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-for-detection-instructions.pdf<br>Contents: Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus - Instructions for Use<br>PDF Title: Tobacco Specific Nitrosamines in Smoke</li>
<li>URL: https://cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf<br>Contents: 2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes<br>PDF Title: Avian H7 (Eurasian Lineage) Influenza Real-time RT-PCR Panel Primer Probes</li>
</ul>
<div class="list-section"><h4>CDC's description of the state of affairs</h4></div>
<ul>
<li><img class="sb-favicon" src="https://emergency.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://emergency.cdc.gov/han/han00426.asp" target="_blank">HAN Archive - 00426 | Health Alert Network (HAN)</a></li>
<li><img class="sb-favicon" src="https://emergency.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://emergency.cdc.gov/han/han00427.asp" target="_blank">HAN Archive - 00427 | Health Alert Network (HAN)</a></li>
<li><img class="sb-favicon" src="https://www.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://www.cdc.gov/coronavirus/2019-ncov/lab/tool-virus-requests.html" target="_blank">Information for Laboratories COVID-19 Requests for Diagnostic Panels and Virus</a></li>
<li><img class="sb-favicon" src="https://www.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html" target="_blank">Information for Laboratories: 2019-nCoV | CDC</a></li>
<li><img class="sb-favicon" src="https://www.cdc.gov/TemplatePackage/4.0/assets/imgs/favicon.ico"><a href="https://www.cdc.gov/mmwr/volumes/69/wr/mm6908e1.htm" target="_blank">Update: Public Health Response to the Coronavirus Disease 2019 Outbreak | MMWR</a></li>
</ul>
</div>
<details><summary>2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes - HTML</summary>
<div class="table-responsive"><table class="table table-bordered table-striped bg-gray-l3"><caption class="sr-only">2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes</caption><thead class="thead-dark"><tr><th scope="col">Name</th><th scope="col">Description</th><th scope="col">Oligonucleotide Sequence (5’>3’)</th><th scope="col">Label1</th><th scope="col">Working<br> Conc.</th></tr></thead><tbody><tr><td scope="row">2019-nCoV_N1-F</td><td>2019-nCoV_N1 Forward Primer</td><td>5’-GAC CCC AAA ATC AGC GAA AT-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N1-R</td><td>2019-nCoV_N1 Reverse Primer</td><td>5’-TCT GGT TAC TGC CAG TTG AAT CTG-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N1-P</td><td>2019-nCoV_N1 Probe</td><td>5’-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1-3’</td><td>FAM, BHQ-1</td><td>5 µM</td></tr><tr><td scope="row">2019-nCoV_N2-F</td><td>2019-nCoV_N2 Forward Primer</td><td>5’-TTA CAA ACA TTG GCC GCA AA-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N2-R</td><td>2019-nCoV_N2 Reverse Primer</td><td>5’-GCG CGA CAT TCC GAA GAA-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N2-P</td><td>2019-nCoV_N2 Probe</td><td>5’-FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1-3’</td><td>FAM, BHQ-1</td><td>5 µM</td></tr><tr><td scope="row">2019-nCoV_N3-F</td><td>2019-nCoV_N3 Forward Primer</td><td>5’-GGG AGC CTT GAA TAC ACC AAA A-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N3-R</td><td>2019-nCoV_N3 Reverse Primer</td><td>5’-TGT AGC ACG ATT GCA GCA TTG-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">2019-nCoV_N3-P</td><td>2019-nCoV_N3 Probe</td><td>5’-FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1-3’</td><td>FAM, BHQ-1</td><td>5 µM</td></tr><tr><td scope="row">RP-F</td><td>RNAse P Forward Primer</td><td>5’-AGA TTT GGA CCT GCG AGC G-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">RP-R</td><td>RNAse P Reverse Primer</td><td>5’-GAG CGG CTG TCT CCA CAA GT-3’</td><td>None</td><td>20 µM</td></tr><tr><td scope="row">RP-P</td><td>RNAse P<br> Probe</td><td>5’-FAM – TTC TGA CCT GAA GGC TCT GCG CG – BHQ-1-3’</td><td>FAM, BHQ-1</td><td>5 µM</td></tr></tbody></table></div>
</details>
<details><summary>2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes - PDF</summary>
<iframe src="https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf" type='application/pdf' width='700px' height='800px'></iframe>
</details>
## Vaccines
### [feraliscatus/VxAfee]
An open source personalized peptide vaccine being designed to work against 2019-nCoV. It might be interesting to test this in-vitro against a cell culture to determine what type of response there is using an ELISPOT assay.
---
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[charite.de]: https://hackmd.io/@jcahill/SJ7nStBNL#charitede
[chinacdc.cn]: https://hackmd.io/@jcahill/SJ7nStBNL#chinacdccn
[cdc.gov - Testing Issues - Mainstream Reporting]: https://hackmd.io/@jcahill/SJ7nStBNL#cdcgov---Testing-Issues---Mainstream-Reporting
[cdc.gov - Testing Protocols and Primers]: https://hackmd.io/@jcahill/SJ7nStBNL#cdcgov---Testing-Protocols-and-Primers
[hku.hk]: https://hackmd.io/@jcahill/SJ7nStBNL#fightcovidhkuhk-medhkuhk
[niid.go.jp]: https://hackmd.io/@jcahill/SJ7nStBNL#niidgojp
[nih.moph.go.th]: https://hackmd.io/@jcahill/SJ7nStBNL#nihmophgoth
[other .gov (US)]: https://hackmd.io/@jcahill/SJ7nStBNL#other-gov-US
[WHO Protocols List - Notes by country/institute]: https://hackmd.io/@jcahill/SJ7nStBNL#WHO-Protocols-List---Notes-by-countryinstitute1
[CDC Bungled Test Kit]: https://hackmd.io/@jcahill/SJ7nStBNL#CDC-Bungled-Test-Kit
[Vaccines]: https://hackmd.io/@jcahill/SJ7nStBNL#Vaccines
<!-- Links - OpenCell -->
[opencell_01]: https://twitter.com/mugecevik/status/1222164778069700618
[opencell_02]: https://www.elsevier.com/life-sciences/journals/modelling-epidemics-the-maths-behind-disease-outbreaks
[opencell_03]: https://github.com/s-andrews/virusbreak
[opencell_04]: https://www.ndemiccreations.com/en/22-plague-inc
[opencell_05]: http://www.gleamviz.org/simulator
[opencell_06]: http://www.shanghaitech.edu.cn/2020/0126/c1001a50145/page.htm
[opencell_07]: http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=AEEEF9C0
[opencell_08]: https://www.biorxiv.org/content/10.1101/2020.01.24.919241v3
[opencell_09]: http://glue-tools.cvr.gla.ac.uk/#/home
[opencell_10]: https://github.com/giffordlabcvr
[opencell_11]: http://nglviewer.org/#nglview
[opencell_12]: http://www.choderalab.org/research-projects/automated-ligand-design
[opencell_13]: https://www.bakerlab.org
[opencell_14]: https://www.rosettacommons.org
[opencell_15]: https://collinslab.mit.edu/files/cell_pardee3.pdf
[opencell_16]: https://collinslab.mit.edu/files/cell_pardee2.pdf
[opencell_17]: https://collinslab.mit.edu/publications.html
[opencell_18]: https://www.pardeelab.org/publications.html
[opencell_19]: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196484
[opencell_20]: http://www.justbiotherapeutics.com/technology
<!-- Links - Other threads in Biohacking and Genetic Design Network -->
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[1551677334970946]: https://www.facebook.com/groups/769326966539324/permalink/1551677334970946
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[1552794401525906]: https://www.facebook.com/groups/769326966539324/permalink/1552794401525906
[1556781941127152]: https://www.facebook.com/groups/769326966539324/permalink/1556781941127152
[1573924052746274]: https://www.facebook.com/groups/geneticbiohacking/permalink/1573924052746274
[1576195075852505]: https://www.facebook.com/groups/geneticbiohacking/permalink/1576195075852505
[1577925299012816]: https://www.facebook.com/groups/geneticbiohacking/permalink/1577925299012816
[1577981212340558]: https://www.facebook.com/groups/geneticbiohacking/permalink/1577981212340558
[1578910642247615]: https://www.facebook.com/groups/geneticbiohacking/permalink/1578910642247615
[1581425731996106]: https://www.facebook.com/groups/geneticbiohacking/permalink/1581425731996106
[1582033708601975]: https://www.facebook.com/groups/geneticbiohacking/permalink/1582033708601975
[1583364041802275]: https://www.facebook.com/groups/geneticbiohacking/permalink/1583364041802275
[1585257061612973]: https://www.facebook.com/groups/geneticbiohacking/permalink/1585257061612973
[1586670104805002]: https://www.facebook.com/groups/geneticbiohacking/permalink/1586670104805002
[1587933708011975]: https://www.facebook.com/groups/geneticbiohacking/permalink/1587933708011975
[1588518901286789]: https://www.facebook.com/groups/geneticbiohacking/permalink/1588518901286789
[1588875774584435]: https://www.facebook.com/groups/geneticbiohacking/permalink/1588875774584435
[1588958661242813]: https://www.facebook.com/groups/geneticbiohacking/permalink/1588958661242813
<!-- Links - Testing -->
[HKU (Peiris et al.) - Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR]: https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf
<!-- Links - Vaccines -->
[feraliscatus/VxAfee]: https://github.com/feraliscatus/VxAfee
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